| 1. |
- Adamovic, Nadja, et al.
(författare)
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European Materials Modelling Council
- 2017
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Ingår i: Proceedings Of The 4Th World Congress On Integrated Computational Materials Engineering (Icme 2017). - Cham : Springer Publishing Company. - 9783319578644 - 9783319578637 ; , s. 79-92
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Konferensbidrag (refereegranskat)abstract
- The aim of the European Materials Modelling Council (EMMC) is to establish current and forward looking complementary activities necessary to bring the field of materials modelling closer to the demands of manufacturers (both small and large enterprises) in Europe. The ultimate goal is that materials modelling and simulation will become an integral part of product life cycle management in European industry, thereby making a strong contribution to enhance innovation and competitiveness on a global level. Based on intensive efforts in the past two years within the EMMC, which included numerous consultation and networking actions with representatives of all stakeholders including Modellers, Software Owners, Translators and Manufacturers in Europe, the EMMC identified and proposed a set of underpinning and enabling actions to increase the industrial exploitation of materials modelling in Europe. EMMC will pursue the following overarching objectives in order to bridge the gap between academic innovation and industrial application: enhance the interaction and collaboration between all stakeholders engaged in different types of materials modelling, including modellers, software owners, translators and manufacturers, facilitate integrated materials modelling in Europe building on strong and coherent foundations, coordinate and support actors and mechanisms that enable rapid transfer of materials modelling from academic innovation to the end users and potential beneficiaries in industry, achieve greater awareness and uptake of materials modelling in industry, in particular SMEs, elaborate Roadmaps that (i) identify major obstacles to widening the use of materials modelling and (ii) elaborate strategies to overcome them.
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| 2. |
- Agosta, Lorenzo, et al.
(författare)
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Adsorption of Glycine on TiO2 in Water from On-the-fly Free-Energy Calculations and In Situ Electrochemical Impedance Spectroscopy
- 2024
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Ingår i: Langmuir. - 0743-7463 .- 1520-5827. ; 40:23, s. 12009-12016
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Tidskriftsartikel (refereegranskat)abstract
- We report here an experimental-computational study of hydrated TiO2 anatase nanoparticles interacting with glycine, where we obtain quantitative agreement of the measured adsorption free energies. Ab initio simulations are performed within the tight binding and density functional theory in combination with enhanced free-energy sampling techniques, which exploit the thermodynamic integration of the unbiased mean forces collected on-the-fly along the molecular dynamics trajectories. The experiments adopt a new and efficient setup for electrochemical impedance spectroscopy measurements based on portable screen-printed gold electrodes, which allows fast and in situ signal assessment. The measured adsorption free energy is −30 kJ/mol (both from experiment and calculation), with preferential interaction of the charged group which strongly adsorbs on the TiO2 bridging oxygens. This highlights the importance of the terminal amino groups in the adsorption mechanism of amino acids on hydrated metal oxides. The excellent agreement between computation and experiment for this amino acid opens the doors to the exploration of the interaction free energies for other moderately complex bionano systems.
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| 3. |
- Agosta, Lorenzo, et al.
(författare)
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Origin of the Hydrophobic Behaviour of Hydrophilic CeO2
- 2023
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Ingår i: Angewandte Chemie International Edition. - : Wiley-VCH Verlagsgesellschaft. - 1433-7851 .- 1521-3773. ; 62:35
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Tidskriftsartikel (refereegranskat)abstract
- The nature of the hydrophobicity found in rare-earth oxides is intriguing. The CeO2 (100) surface, despite its strongly hydrophilic nature, exhibits hydrophobic behaviour when immersed in water. In order to understand this puzzling and counter-intuitive effect we performed a detailed analysis of the water structure and dynamics. We report here an ab-initio molecular dynamics simulation (AIMD) study which demonstrates that the first water layer, in immediate contact with the hydroxylated CeO2 surface, is responsible for the effect behaving as a hydrophobic interface with respect to the rest of the liquid water. The hydrophobicity is manifested in several ways: a considerable diffusion enhancement of the confined liquid water as compared with bulk water at the same thermodynamic condition, a weak adhesion energy and few H-bonds above the hydrophobic water layer, which may also sustain a water droplet. These findings introduce a new concept in water/rare-earth oxide interfaces: hydrophobicity mediated by specific water patterns on a hydrophilic surface.
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| 4. |
- Agosta, Lorenzo, et al.
(författare)
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Supercooled liquid-like dynamics in water near a fully hydrated titania surface : Decoupling of rotational and translational diffusion
- 2021
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 154:9
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Tidskriftsartikel (refereegranskat)abstract
- We report an ab initio molecular dynamics (MD) simulation investigating the effect of a fully hydrated surface of TiO2 on the water dynamics. It is found that the universal relation between the rotational and translational diffusion characteristics of bulk water is broken in the water layers near the surface with the rotational diffusion demonstrating progressive retardation relative to the translational diffusion when approaching the surface. This kind of rotation-translation decoupling has so far only been observed in the supercooled liquids approaching glass transition, and its observation in water at a normal liquid temperature is of conceptual interest. This finding is also of interest for the application-significant studies of the water interaction with fully hydrated nanoparticles. We note that this is the first observation of rotation-translation decoupling in an ab initio MD simulation of water.
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| 5. |
- Ahlstrand, Emma, et al.
(författare)
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Interaction energies between metal ions (Zn2+ and Cd2+) and biologically relevant ligands
- 2013
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Ingår i: International Journal of Quantum Chemistry. - Hoboken, NJ : Wiley. - 0020-7608 .- 1097-461X. ; 113:23, s. 2554-2562
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Tidskriftsartikel (refereegranskat)abstract
- Interactions between the group XII metals Zn2+ and Cd2+ and amino acid residues play an important role in biology due to the prevalence of the first and the toxicity of the second. Estimates of the interaction energies between the ions and relevant residues in proteins are however difficult to obtain. This study reports on calculated interaction energy curves for small complexes of Zn2+ or Cd2+ and amino acid mimics (acetate, methanethiolate, and imidazole) or water. Given that many applications and models (e.g., force fields, solvation models, etc.) begin with and rely on an accurate description of gas-phase interaction energies, this is where our focus lies in this study. Four density functional theory (DFT)-functionals and MP2 were used to calculate the interaction energies not only at the respective equilibrium distances but also at a relevant range of ion–ligand separation distances. The calculated values were compared with those obtained by CCSD(T). All DFT-methods are found to overestimate the magnitude of the interaction energy compared to the CCSD(T) reference values. The deviation was analyzed in terms of energy components from localized molecular orbital energy decomposition analysis scheme and is mostly attributed to overestimation of the polarization energy. MP2 shows good agreement with CCSD(T) [root mean square error (RMSE) = 1.2 kcal/mol] for the eight studied complexes at equilibrium distance. Dispersion energy differences at longer separation give rise to increased deviations between MP2 and CCSD(T) (RMSE = 6.4 kcal/mol at 3.0 Å). Overall, the results call for caution in applying DFT methods to metalloprotein model complexes even with closed-shell metal ions such as Zn2+ and Cd2+, in particular at ion–ligand separations that are longer than the equilibrium distances.
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| 6. |
- Ahlstrand, Emma, et al.
(författare)
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Interaction Energies in Complexes of Zn and Amino Acids : A Comparison of Ab Initio and Force Field Based Calculations
- 2017
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 121:13, s. 2643-2654
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Tidskriftsartikel (refereegranskat)abstract
- Zinc plays important roles in structural stabilization of proteins, eniyine catalysis, and signal transduction. Many Zn binding sites are located at the interface between the protein and the cellular fluid. In aqueous solutions, Zn ions adopt an octahedral coordination, while in proteins zinc can have different coordinations, with a tetrahedral conformation found most frequently. The dynainics of Zn binding to proteins and the formation of complexes that involve Zn are dictated by interactions between Zn and its binding partners. We calculated the interaction energies between Zn and its ligands in complexes that mimic protein binding sites and in Zn complexes of water and one or two amino acid moieties, using quantum mechanics (QM) and molecular mechanics (MM). It was found that MM calculations that neglect or only approximate polarizability did not reproduce even the relative order of the QM interaction energies in these complexes. Interaction energies calculated with the CHARMM-Diode polarizable force field agreed better with the ab initio results,:although the deviations between QM and MM were still rather large (40-96 kcallmol). In order to gain further insight into Zn ligand interactions, the free energies of interaction were estimated by QM calculations with continuum solvent representation, and we performed energy decomposition analysis calculations to examine the characteristics of the different complexes. The ligand-types were found to have high impact on the relative strength of polarization and electrostatic interactions. Interestingly, ligand ligand interactions did not play a significant role in the binding of Zn. Finally) analysis of ligand exchange energies suggests that carboxylates could be exchanged with water molecules, which explains the flexibility in Zn:binding dynamics. An exchange between earboxylate (Asp/Glii) and imidazole (His) is less likely.
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| 7. |
- Aldongarov, Anuar, et al.
(författare)
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Theoretical study on passivation of small CdS clusters
- 2014
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Ingår i: Molecular Physics. - : Taylor & Francis. - 0026-8976 .- 1362-3028. ; 112:5-6, s. 674-682
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Tidskriftsartikel (refereegranskat)abstract
- We use density functional theory quantum chemical calculations to model optical properties of small cadmium sulphide clusters in order to explore the formation of trap states and the possibility to achieve surface passivation. The addition of capping oxygen ions on the surface of the CdS quantum dots is found to passivate the single-bonded Cd atoms. Added Cu ions resulted in the formation of deep trap states for certain locations of the copper impurity, while removal of single-bonded Cd atoms by adding S or SH groups leads to a band gap increase.
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| 8. |
- Alfredsson, Maria, et al.
(författare)
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A comparison of Hartree-Fock, MP2, and DFT results for the HCN dimer and crystal
- 1996
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Ingår i: INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY. ; 60:3, s. 767-777
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Tidskriftsartikel (refereegranskat)abstract
- A number of hydrogen-bond related quantities-geometries, interaction energies, dipole moments, dipole moment derivatives, and harmonic vibrational frequencies-were calculated at the Hartree-Fock, MP2, and different DFT levels for the HCN dimer and the pe
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| 9. |
- Alfredsson, M, et al.
(författare)
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Hartree-Fock and DFT calculations of quadrupole coupling constants in water clusters and ice
- 1999
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Ingår i: CHEMICAL PHYSICS. - 0301-0104. ; 242:2, s. 161-175
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Periodic ab initio calculations of the O-17 and H-2 quadrupole coupling constants (QCC) and their shifts have been performed for ice VIII and ice IX. Cluster calculations were done for smaller water clusters and chains. The ice Vm crystal structure was op
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| 10. |
- Alfredsson, M., et al.
(författare)
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OH frequency calculations for the hydroxylated MgO(001) surface
- 2002
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Ingår i: Molecular Simulation. - : Informa UK Limited. - 0892-7022 .- 1029-0435. ; 28:07-jun, s. 663-681
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Tidskriftsartikel (refereegranskat)abstract
- We have performed periodic Hartree-Fock calculations for OH groups adsorbed on the MgO(001) surface considering different surface coverages. Six types of OH groups are discussed: OH-, OH, H+, H and hydrogen-bonded OH and H. It is found that when both OH and H are present on the surface, the two groups are best described as OH-. We suggest that the highest-frequency fundamental band (similar to3750 cm(-1) in the experimental OH spectrum) is assigned to OH- groups adsorbed on top of Mg2+, while H+ adsorbed on top of O2- give rise to the broader band at similar to3550 cm(-1).
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